BCAT1 p.Tyr374=
c.1122T>C · rs756053143 · VCV3042288
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
Conditions
1
BCAT1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.38 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -3.1 |
| Overall | ||
| CADD | 0.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,070 alleles
Filtering AF
0.00581%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00372%
Overall
0.00434%
70/1,612,966 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,035 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,478 |
| European (non-Finnish) | 0.00517% | 19,334 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,560 |
| Admixed American | 0.00167% | 59,892 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BCAT1
- Protein
- p.Tyr374=
- Coding
- c.1122T>C
- MANE Select
- NM_005504
- dbSNP
- rs756053143
- Type
- single nucleotide variant
- Location
- chr12:24818047 (GRCh38)
- Gene constraint
- LOEUF 1.219 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.05 · 17 PDB
Disease context
BCAT1-related disorder
Similar variants
- BCAT1 c.7-72C>T Benign same condition
- BCAT1 p.Glu348Lys Likely benign same condition
- BCAT1 p.Leu344= Likely benign same condition
- BCAT1 p.Ser379= Benign same condition
- BCAT1 p.Thr59Met Likely benign ⚠ same condition
- BCAT1 p.Thr13= Benign ★★ same type
- BCAT1 c.7-1070G>A Uncertain significance ★ same type
- BCAT1 c.7-1075C>T Uncertain significance ★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bcat1-p-tyr374 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown